def cli(ctx, basepath, workflow_name, step, save, use_input): ctx.obj["structure"] = Structure(basepath=basepath, name=workflow_name, step=step) ctx.obj["json"] = False ctx.obj["save"] = save ctx.obj["use_input"] = use_input
def cli(ctx, basepath, workflow_name, step, save, use_input, prototype_cache_preloaded_only): ctx.obj["structure"] = Structure(basepath=basepath, name=workflow_name, step=step) ctx.obj["json"] = True ctx.obj["save"] = save ctx.obj["use_input"] = use_input ctx.obj["prototype_cache_preloaded_only"] = prototype_cache_preloaded_only
def cli(ctx, basepath, workflow_name, step, save, use_input, configuration): ctx.obj["structure"] = Structure(basepath=basepath, name=workflow_name, step=step) ctx.obj["save"] = save ctx.obj["use_input"] = use_input config_module = ctx.obj["structure"].configuration_module() importlib.import_module(config_module) configdict = sys.modules[config_module] ctx.obj["configurations"] = configdict.configurations
def cli(ctx, basepath, workflow_name, step, configuration, save, use_input): ctx.obj["structure"] = Structure(basepath=basepath, name=workflow_name, step=step) ctx.obj["json"] = True ctx.obj["save"] = save ctx.obj["use_input"] = use_input configdict = {} execfile(configuration or ctx.obj["structure"].configuration_file_path(), configdict) ctx.obj["configurations"] = configdict["configurations"][:]
def cli(ctx, basepath, workflow_name, step, configuration, start, maximum, json, hdf, save, use_input): if not hdf and json: ctx.obj["json"] = True else: ctx.obj["hdf"] = hdf ctx.obj["json"] = json if ctx.obj.get("json", False): ctx.obj["file_type"] = "json" elif ctx.obj.get("hdf", False): ctx.obj["file_type"] = "h5" ctx.obj["save"] = save ctx.obj["use_input"] = use_input ctx.obj["start"] = start ctx.obj["maximum"] = maximum ctx.obj["structure"] = Structure(basepath=basepath, name=workflow_name, step=step) config_module = ctx.obj["structure"].configuration_module() importlib.import_module(config_module) configdict = sys.modules[config_module] ctx.obj["configurations"] = configdict.configurations
def cli(ctx, basepath, workflow_name, step, use_input): ctx.obj["structure"] = Structure(basepath=basepath, name=workflow_name, step=step) ctx.obj["use_input"] = use_input
def start(start, end): env_vars = json.load( open( os.path.join(os.path.dirname(__file__), os.pardir, "base_configuration.json"), "r")) env_vars.update( json.load( open( os.path.join(os.path.dirname(__file__), "workflow_configuration.json"), "r"))) if env_vars["DISS_BASEPATH"].startswith( "./") or env_vars["DISS_BASEPATH"] == ".": env_vars["DISS_BASEPATH"] = os.path.abspath( os.path.join(os.path.dirname(__file__), os.pardir, env_vars["DISS_BASEPATH"][1:])) if env_vars["DISS_BASEPATH"] == "..": env_vars["DISS_BASEPATH"] = os.path.abspath( os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, env_vars["DISS_BASEPATH"][2:])) if env_vars["DISS_WORKFLOWFOLDER_NAME"] == ".": env_vars["DISS_WORKFLOWFOLDER_NAME"] = os.path.basename( os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir))) workflow = Workflow() workflow.add_task( cli_path=Structure.data_selection_cli(), cmd="index-valid-hdf-trees", save=True, pcount=1, trees=[ os.path.join( os.path.dirname(__file__), os.pardir, "data/trees/Bd_Kpi_mdst_000001_prod00006875_task00000001.h5"), os.path.join( os.path.dirname(__file__), os.pardir, "data/trees/Bd_Kspi0_mdst_000001_prod00006201_task00000001.h5") ], name="Index valid HDF trees") workflow.prepare_intermediate_as_input(reference="Index valid HDF trees") workflow.add_task(cli_path=Structure.workflow_cli(), cmd="process-as-matrix", save=True, hdf=True, use_input=True, name="Generate Distance Matrix", pcount=16) workflow.add_task( cli_path=Structure.data_selection_cli(), cmd="index-valid-hdf-trees", save=True, pcount=1, representatives=[ os.path.join( os.path.dirname(__file__), os.pardir, "data/trees/Bd_Kpi_mdst_000001_prod00006875_task00000001.h5"), os.path.join( os.path.dirname(__file__), os.pardir, "data/trees/Bd_Kspi0_mdst_000001_prod00006201_task00000001.h5") ], trees=[ os.path.join(os.path.dirname(__file__), os.pardir, "data/trees/toy_B-Kpi/1110020000_Kpi_Dplus.h5"), os.path.join(os.path.dirname(__file__), os.pardir, "data/trees/toy_B-Kpi/1110020000_Kpi_Dstar.h5"), os.path.join(os.path.dirname(__file__), os.pardir, "data/trees/toy_B-Kpi/1110026100_Kspi0_Dplus.h5"), os.path.join(os.path.dirname(__file__), os.pardir, "data/trees/toy_B-Kpi/1110026100_Kspi0_Dstar.h5") ], name="Index trees and representatives") workflow.prepare_intermediate_as_input( reference="Index trees and representatives") workflow.add_task(cli_path=Structure.workflow_cli(), cmd="batch-process-as-vector", save=True, hdf=True, use_input=True, name="Generate Distance Vectors", pcount=16) # finalise results workflow.finalise(file_type="h5", reference="Generate Distance Matrix") workflow.finalise(file_type="h5", reference="Generate Distance Vectors") workflow.execute(env_vars, start=start, end=end)
def cli(ctx, basepath, workflow_name, step): ctx.obj["structure"] = Structure(basepath=basepath, name=workflow_name, step=step)